Additional file 6 of Metabolic modeling of microbial communities in the chicken ceca reveals a landscape of competition and co-operation
Bibliographic record
Abstract
Supplementary Material 6. Supplementary Figure 6. Non-dietary metabolite exchanges across all 227 taxa in HB and NB communities. A. The heatmap displays the normalized total interactions involving non-dietary metabolites exchanged between 227 taxa across 33 chicken cecum samples. Interactions were normalized by the number of samples in which each cross-feeding pair was present and are color-coded by interaction frequency. Taxa are color-coded based on their taxonomic families, interaction frequencies are indicated by color intensity. Taxa on y-axis are grouped by their presence in HB only, NB only, or both; color-coded. Distinct cliques of interacting species are highlighted in red boxes (A-H), which were selected based on visual inspection of the hierarchically clustered heatmap to identify the largest and most distinct clusters of taxa with similar interaction patterns. B. The upset plot summarizes the unique and shared non-dietary metabolites exchanged within the investigated cliques (A-H) highlighted in panel A. Each bar represents the number of metabolites exchanged, with intersections indicating metabolites shared between multiple cliques. Some metabolite names have been shortened or modified for clarity in the figure. The following abbreviations are used: 2-Oxoglut for 2-Oxoglutarate, Ddca for dodecanoic acid, L-Asp for L-Aspartate, Glu for Glutamate, D-Lact and L-Lact for D- and L-Lactate, respectively, NAD for nicotinamide adenosine dinucleotide, Propion for propionate, Pyro-P for pyrophosphate, and Putrsc for putrescine.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.009 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.002 |
| Bibliometrics | 0.002 | 0.003 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.003 | 0.002 |
| Open science | 0.003 | 0.001 |
| Research integrity | 0.002 | 0.001 |
| Insufficient payload (model declined to judge) | 0.789 | 0.170 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; the direct Gemma label and the distilled Codex classifier agree on what is shown here.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".